Background: Anorectal pain is a symptom which may have both structural and functional causes, and can, sometimes, develop into a chronic pain syndrome. Functional causes in particular are challenging to treat when conservative treatment measures fail. Botulinum toxin A (BTX-A) can be applied to relax the anal sphincter and/or levator ani muscle to break the vicious circle of pain and contraction. In our tertiary referral proctology clinic, we evaluated the outcome of patients treated with BTX-A for chronic functional anorectal pain. Methods: Our electronic database was searched for patients who had BTX-A treatment for chronic functional anorectal pain from 2011 to 2016. All medical data concerning history, treatments, and clinical outcome were retrieved. The clinical outcome (resolution of pain) was scored as good, temporary, or poor. Results: A total of 113 patients [47 (42%) males; age 51years, SD 13 years, range 18–88 years] with chronic functional anorectal pain were included. The outcome of BTX-A treatment was good in 53 (47%), temporary in 23 (20%), and poor in 37 (33%). To achieve this outcome, 29 (45%) patients needed a single treatment, 11 (44%) a second treatment, and 13 (54%) ≥ 3 treatments. Conclusions: Chronic functional anorectal pain can be treated successfully with BTX-A in 47% of patients who fail conservative management. Repeated injections may be needed to ensure complete cure in a subgroup of patients.